Having been closed and partly demolished, the church was rebuilt and served its congregation whilst the city slowly changed around it.

Rebirth

St Helen's today occupies a very prominent position facing an open square opposite the imposing facade of the Mansion House. Those were not there in the 1550s, but nevertheless St Helen's clearly had an importance in the cityscape. Following the sale in 1551-2 and partial demolition, an Act was obtained in 1553-4 to reinstate the church, because it had stood in a 'principal place', and its suppression had 'defaced and deformed' the city. The present north arcade is thought to belong to the 1550s, and in 1558 money was left towards rebuilding the steeple which consisted of a bell-turret supported on a large over-arch crowning the west gable.

Seventeenth and eighteenth centuries

Economic changes particularly in the cloth trade in the late fifteenth century had important consequences for York, although it remained for a time the principal city of the north of England and the seat of the Council of the North until 1641. The Civil War and the siege of 1644 further undermined the economy and it was only with the development of the city as a fashionable resort and residential town in the eighteenth century that fortunes again improved. There were many fine estates and houses in Yorkshire, often funded with wealth from trade and industry, and York became a logical alternative to London or Bath as a place to spend the season. This led to the re-development of areas near the church, notably the Mansion House facing St Helen and the Assembly Rooms in Blake Street. Part of those improvements included purchase of the churchyard by the city Corporation to form what is now St Helen's Square, so linking Davygate with Blake Street. Like many old city churchyards it was several feet high from centuries of burials, a path already ran across it, and the intersection of Coney Street with Stonegate was known as Cuckold's Corner, suggesting an unsavoury reputation. A small plot was provided in Davygate as a new burial ground, where it still exists, and the square was paved in 1745. Further street improvements were carried out in about 1796, when the southwest corner of the church was realigned to enable the street to be widened.

Development of the churchyard provided an opportunity to raise the floor level in the church. Before then access must have been inconvenient, because it was necessary to climb steps into the churchyard and then descend into the church which by then was below the street. There were twelve steps up to the font. Changing the floor level was easy enough, since there was a large quantity of earth to remove from the churchyard and the church the nearest place to deposit it. Unfortunately, because like very many churches the building was ceilinged, the effect was to create a low space very different from the lofty interior of today. In all St Helen's did not benefit a great deal from the developments close by. There were other, grander and more fashionable, churches such as St Martin Coney Street. The low income of the vicar, which depended largely on past endowments, would have made it difficult to attract clergy of the first order although the church did benefit from Queen Anne's Bounty in 1757. The impression is of a church which by the end of the eighteenth century was in a rather sorry state.